genesis/pipeline.py

# genesis/pipeline.py
"""
GENESIS-AI Research Pipeline
Coordinates ontology expansion, literature retrieval, summaries, citations, structure fetching, graphDB storage, and narration.
"""

import os
from datetime import datetime

from .ontology import expand_terms_with_ontology
from .molecule_viewer import fetch_structure
from .narration import narrate_text
from .providers import (
    run_deepseek_summary,
    run_gemini_polish,
    run_openai_image,
    pubmed_fallback_search
)
from .graphdb import write_topic_and_papers

# ENV
ELEVEN_LABS_API_KEY = os.getenv("ELEVEN_LABS_API_KEY")
GEMINI_API_KEY = os.getenv("GEMINI_API_KEY")
NEO4J_URI = os.getenv("NEO4J_URI")

SYNBIO_MODE = True

def synthetic_biology_prompt_inject(query, expanded_terms):
    """Injects domain-specific bias toward synthetic biology research."""
    context = (
        "You are an expert in synthetic biology. Focus on CRISPR, metabolic engineering, "
        "living therapeutics, protein design, biosensors, and biosecurity. Include literature, "
        "structures, market trends, and regulatory insights with citations."
    )
    return f"{context}\n\nQuery: {query}\nExpanded terms: {', '.join(expanded_terms)}"

def research_once(query, graph_preview=True, narration=True):
    """Runs the GENESIS-AI pipeline for a given research query."""
    
    # 1. Expand ontology
    expanded_terms = expand_terms_with_ontology(query)

    # 2. Domain injection
    enriched_query = synthetic_biology_prompt_inject(query, expanded_terms) if SYNBIO_MODE else query

    # 3. Summarize (DeepSeek)
    summary_raw = run_deepseek_summary(enriched_query)

    # 4. Polish (Gemini)
    summary_polished = run_gemini_polish(summary_raw)

    # 5. Citations
    citations = pubmed_fallback_search(query)

    # 6. Structures
    structures = [fetch_structure(term) for term in expanded_terms]

    # 7. Visual (OpenAI Image)
    image_url = run_openai_image(query)

    # 8. GraphDB
    if graph_preview and NEO4J_URI:
        write_topic_and_papers(query, citations, expanded_terms)

    # 9. Narration
    audio_url = narrate_text(summary_polished) if narration and ELEVEN_LABS_API_KEY else None

    # 10. Output
    return {
        "timestamp": datetime.utcnow().isoformat(),
        "query": query,
        "expanded_terms": expanded_terms,
        "summary": summary_polished,
        "citations": citations,
        "structures": structures,
        "image_url": image_url,
        "audio_url": audio_url
    }